Merge pull request #15079 from jmchilton/tool_test_typing

Type some of tool test parsing code.

lib/galaxy/tool_util/parser/interface.py

@@ -7,19 +7,46 @@ from abc import (
 )
 from os.path import join
 from typing import (
+    Any,
     Dict,
     List,
     Optional,
     Tuple,
+    Union,
 )
 
 import packaging.version
+from typing_extensions import TypedDict
 
 from galaxy.util.path import safe_walk
 from .util import _parse_name
 
 NOT_IMPLEMENTED_MESSAGE = "Galaxy tool format does not yet support this tool feature."
 
+AssertionDict = TypedDict(
+    "AssertionDict", {"tag": str, "attributes": Dict[str, Any], "children": Optional[List[Dict[str, Any]]]}
+)
+AssertionList = Optional[List[AssertionDict]]
+XmlInt = Union[str, int]
+ToolSourceTest = TypedDict(
+    "ToolSourceTest",
+    {
+        "inputs": Any,
+        "outputs": Any,
+        "output_collections": List[Any],
+        "stdout": AssertionList,
+        "stderr": AssertionList,
+        "expect_exit_code": Optional[XmlInt],
+        "expect_failure": bool,
+        "expect_test_failure": bool,
+        "maxseconds": Optional[XmlInt],
+        "expect_num_outputs": Optional[XmlInt],
+        "command": AssertionList,
+        "command_version": AssertionList,
+    },
+)
+ToolSourceTests = TypedDict("ToolSourceTests", {"tests": List[ToolSourceTest]})
+
 
 class ToolSource(metaclass=ABCMeta):
     """This interface represents an abstract source to parse tool
@@ -268,7 +295,7 @@ class ToolSource(metaclass=ABCMeta):
             paths_and_modtimes[self.source_path] = os.path.getmtime(self.source_path)
         return paths_and_modtimes
 
-    def parse_tests_to_dict(self):
+    def parse_tests_to_dict(self) -> ToolSourceTests:
         return {"tests": []}
 
     def __str__(self):

lib/galaxy/tool_util/parser/xml.py

@@ -3,7 +3,10 @@ import logging
 import math
 import re
 import uuid
-from typing import Optional
+from typing import (
+    List,
+    Optional,
+)
 
 import packaging.version
 
@@ -19,6 +22,7 @@ from galaxy.util import (
     xml_to_string,
 )
 from .interface import (
+    AssertionList,
     InputSource,
     PageSource,
     PagesSource,
@@ -26,6 +30,8 @@ from .interface import (
     TestCollectionDef,
     TestCollectionOutputDef,
     ToolSource,
+    ToolSourceTest,
+    ToolSourceTests,
 )
 from .output_actions import ToolOutputActionGroup
 from .output_collection_def import dataset_collector_descriptions_from_elem
@@ -537,10 +543,10 @@ class XmlToolSource(ToolSource):
     def source_path(self):
         return self._source_path
 
-    def parse_tests_to_dict(self):
+    def parse_tests_to_dict(self) -> ToolSourceTests:
         tests_elem = self.root.find("tests")
-        tests = []
-        rval = dict(tests=tests)
+        tests: List[ToolSourceTest] = []
+        rval: ToolSourceTests = dict(tests=tests)
 
         if tests_elem is not None:
             for i, test_elem in enumerate(tests_elem.findall("test")):
@@ -587,8 +593,8 @@ class XmlToolSource(ToolSource):
         return creators
 
 
-def _test_elem_to_dict(test_elem, i, profile=None):
-    rval = dict(
+def _test_elem_to_dict(test_elem, i, profile=None) -> ToolSourceTest:
+    rval: ToolSourceTest = dict(
         outputs=__parse_output_elems(test_elem),
         output_collections=__parse_output_collection_elems(test_elem, profile=profile),
         inputs=__parse_input_elems(test_elem, i),
@@ -737,7 +743,7 @@ def __parse_assert_list(output_elem):
     return __parse_assert_list_from_elem(assert_elem)
 
 
-def __parse_assert_list_from_elem(assert_elem):
+def __parse_assert_list_from_elem(assert_elem) -> AssertionList:
     assert_list = None
 
     def convert_elem(elem):

lib/galaxy/tool_util/parser/yaml.py

@@ -12,10 +12,14 @@ from galaxy.tool_util.parser.util import (
     DEFAULT_DELTA_FRAC,
 )
 from .interface import (
+    AssertionDict,
+    AssertionList,
     InputSource,
     PageSource,
     PagesSource,
     ToolSource,
+    ToolSourceTest,
+    ToolSourceTests,
 )
 from .output_collection_def import dataset_collector_descriptions_from_output_dict
 from .output_objects import (
@@ -177,9 +181,9 @@ class YamlToolSource(ToolSource):
         )
         return output_collection
 
-    def parse_tests_to_dict(self):
-        tests = []
-        rval = dict(tests=tests)
+    def parse_tests_to_dict(self) -> ToolSourceTests:
+        tests: List[ToolSourceTest] = []
+        rval: ToolSourceTests = dict(tests=tests)
 
         for i, test_dict in enumerate(self.root_dict.get("tests", [])):
             tests.append(_parse_test(i, test_dict))
@@ -206,7 +210,7 @@ class YamlToolSource(ToolSource):
         return json.dumps(self.root_dict)
 
 
-def _parse_test(i, test_dict):
+def _parse_test(i, test_dict) -> ToolSourceTest:
     inputs = test_dict["inputs"]
     if is_dict(inputs):
         new_inputs = []
@@ -231,7 +235,7 @@ def _parse_test(i, test_dict):
             name = output["name"]
             value = output.get("file", None)
             attributes = output
-            new_outputs.append((name, value, attributes))
+            new_outputs.append({"name": name, "value": value, "attributes": attributes})
 
     for output in new_outputs:
         attributes = output["attributes"]
@@ -246,8 +250,6 @@ def _parse_test(i, test_dict):
         attributes["extra_files"] = []
         # TODO
         attributes["metadata"] = {}
-        # TODO
-        assert_list = []
         assert_list = __to_test_assert_list(attributes.get("asserts", []))
         attributes["assert_list"] = assert_list
         _ensure_has(attributes, defaults)
@@ -264,7 +266,7 @@ def _parse_test(i, test_dict):
     return test_dict
 
 
-def __to_test_assert_list(assertions):
+def __to_test_assert_list(assertions) -> AssertionList:
     def expand_dict_form(item):
         key, value = item
         new_value = value.copy()
@@ -274,7 +276,7 @@ def __to_test_assert_list(assertions):
     if is_dict(assertions):
         assertions = map(expand_dict_form, assertions.items())
 
-    assert_list = []
+    assert_list: List[AssertionDict] = []
     for assertion in assertions:
         # TODO: not handling nested assertions correctly,
         # not sure these are used though.
@@ -282,7 +284,7 @@ def __to_test_assert_list(assertions):
         if "children" in assertion:
             children = assertion["children"]
             del assertion["children"]
-        assert_dict = dict(
+        assert_dict: AssertionDict = dict(
             tag=assertion["that"],
             attributes=assertion,
             children=children,